Genomic Architecture and Inheritance of Human Ribosomal RNA Gene Arrays

1. Genomic Architecture and Inheritance of Human Ribosomal RNA Gene Arrays Meiotic and Mitotic Instability Andrew J. Pierce Microbiology, Immunology and Molecular Genetics Graduate Center for Toxicology Markey Cancer Center University of Kentucky MI615

2. Meiosis Requires Genomic Restructuring Gametes Crossing-over and Recombination In Meiosis Adapted from: Morgan T.H., Sturtevant A.H., Muller H.J., and Bridges C.B., "The Mechanism of Mendelian Heredity", 1915 By http://www.accessexcellence.org/RC/VL/GG/comeiosis.html http://biology-pages.info Photomicrograph by Prof. Bernard John

3. Some Genomic Disorders Mediated by Repetitive Sequences Complex structure of selected low-copy repeats (LCRs). Horizontal lines represent specific genomic regions with the centromere toward the left and telomere to the right. At the right are listed abbreviations for the disease manifested through common deletions of the regions. The colored regions refer to LCRs with the orientation given by the arrowhead. Note complex structure of LCRs consisting of both direct and inverted repeats. (a) LCRs in chromosome 2q13 responsible for rearrangements associated with familial juvenile nephronophthisis 1 (NPHP1). (b) LCRs7 flanking the Williams–Beuren syndrome (WBS) chromosome region 7q11.23. (c) LCRs15 within the Prader–Willi syndrome/Angelman syndrome (PWS/AS) chromosome region 15q11.2. (d) Smith–Magenis syndrome (SMS) repeats within 17p11.2. (e) LCRs22 within the DiGeorge syndrome (DGS) chromosome 22q11.2. Stankiewicz P, Lupski JR. Genome architecture, rearrangements and genomic disorders. Trends Genet. 2002 Feb;18(2):74-82.

4. Instability Mechanism: Homologous Recombination

5. Instability Mechanism: Homologous Recombination

6. 60S 40S Ribosomal Composition 4 RNA molecules 5S, 5.8S, 28S Nobel Prize 2009! 18S … and 80+ proteins too

7. 5S rDNA Arrays and the Human Genome Project 1

8. Isolate very high molecular weight genomic DNA from human peripheral blood Liberate rDNA arrays by digesting with restriction enzymes that cut external to the array Separate arrays by size on pulsed-field gels Detect rDNA specific bands by Southern blotting Band intensity is proportional to: Length of the array Fraction of cells in the population containing any given sized array bulk genomic DNA bulk genomic DNA Experimental Strategy Repeat Array unit repeat

9. 5S rDNA Arrays from Anonymous Human Donors 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 KB 500 400 300 200 100 50 • Everyone has two different sized arrays • No two people have the same array lengths Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

10. 5S rDNA Arrays from Human Families – Inheritance ARDO PYFI VAGR THAE KB 500 400 300 200 100 50 25 DAD DAD DAD MOM MOM MOM BOY BOY BOY BOY DAD GIRL MOM BOY GIRL Pat. GRANDPA Pat. GRANDMA Mat. GRANDMA Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

12. HindIII NcoI PvuII l l l l5 l4 l DAD DAD DAD MOM MOM MOM BOY BOY BOY BOY BOY BOY 5S rDNA Arrays – Inheritance and Somatic Mosaicism Meiotic rearrangement: Band length not represented in either parent ( dotted circle ) Somatic mosaicism: Band of reduced intensity relative to length ( square bracket ) Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

13. 5S rDNA Arrays – Human Statistics ( N = 27 ) Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

14. 45S Ribosomal DNA in Human Karyotypes http://www.pathology.washington.edu/galleries/Cytogallery/main.php

15. Ribosomal DNA Repeats • generally structured in tandem head-to-tail arrays • unit repeats completely sequenced 45S rDNA repeat 18S 28S Intergenic Spacer 5.8S 43 kilobase pairs Tandem Array of Repeats ( example: 4 x 43kb )

16. 45S rDNA Arrays and the Human Genome Project 13 14 15 21 22

17. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 wells KB 6000 5000 4000 3000 2000 1000 500 45S rDNA Arrays from Anonymous Human Donors Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

18. 45S rDNA Arrays from Human Families – Inheritance ARDO PYFI VAGR THAE wells KB 6000 5000 4000 3000 2000 1000 500 DAD DAD DAD MOM MOM MOM BOY BOY BOY BOY DAD GIRL MOM BOY GIRL Pat. GRANDPA Pat. GRANDMA Mat. GRANDMA Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

19. High Resolution 45S Arrays – Inheritance and Mosaicism ARDO PYFI VAGR THAE wells KB 1000 800 600 400 200 100 50 DAD DAD DAD MOM MOM MOM BOY BOY BOY BOY DAD GIRL MOM BOY GIRL Pat. GRANDPA Pat. GRANDMA Mat. GRANDMA Stults et al. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Research 2008 18(1):13-18.

20. Four Sets of Identical Twins 5S rDNA 45S rDNA 1Mbp - 6Mbp 45S rDNA 50kb - 1Mbp Stults, Killen, Pierce and Pierce (unpublished results)

21. Conclusions • Array lengths vary from person to person • Array lengths are not coordinated between chromosome homologs • Individual arrays are usually inherited in Mendelian manner but undergo meiotic recombination with a frequency of ~10% per array • Mitotic recombination is capable of altering rDNA architecture in different cells in the same person

22. Mitotic Recombination: Chromosomal Instability Syndromes Killen et al. Loss of Bloom syndrome protein destabilizes human gene cluster architecture. 2009 Human Molecular Genetics 18(18):3417-3428.

23. Human Cells are (Mostly) Stable Killen et al. Loss of Bloom syndrome protein destabilizes human gene cluster architecture. 2009 Human Molecular Genetics 18(18):3417-3428.

24. BLM Cells Restructure rDNA Every Cell Division Killen et al. Loss of Bloom syndrome protein destabilizes human gene cluster architecture. 2009 Human Molecular Genetics 18(18):3417-3428.

25. Normal cell metaphase Bloom's syndrome cell metaphase Bloom's Syndrome Amor-Gueret M. Bloom's syndrome. Orphanet Encyclopedia. February 2004 • proportionate pre- and postnatal growth deficiency • sun-sensitive • telangiectatic • hypo- and hyperpigmented skin • chromosomal instability, predisposition to malignancy BLM protein in RecQ-helicase family with Werner Syndrome (WRN), Rothmund-Thomson Syndrome (RecQ4), and two other non-disease-associated members RecQL, RecQ5b

26. Thibodeau SN, Bren G, Schaid D Microsatellite instability in cancer of the proximal colon. Science. 1993 May 7;260(5109):816-9. BLM Primary Cells Show Instability MSI Killen et al. Loss of Bloom syndrome protein destabilizes human gene cluster architecture. 2009 Human Molecular Genetics 18(18):3417-3428.

27. rDNA Clusters Restructured in Half of Solid Tumors Lung & Colorectal Cancer: (39 tumors analyzed) 45% stable 30% preclonal alteration 25% active restructuring Stults et al. Human ribosomal RNA gene clusters are recombinational hotspots in cancer. 2009 Cancer Research 69: 9096-104.